Contacts of the strand formed by residues 311 - 317 (chain H) in PDB entry 1MK9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 311 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227H SER 5.7 0.7 - - - -
309H GLY 4.4 0.2 - - - -
310H VAL* 1.3 71.7 - - - +
312H PHE* 1.3 58.8 + - - +
313H PHE* 4.0 9.6 - - - -
330H LEU 3.5 2.1 - - - +
331H GLY* 3.4 1.6 - - - -
332H ILE* 2.9 33.8 + - - +
391H LEU* 3.9 28.6 - - - +
395H TYR* 6.2 0.2 - - - -
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Residues in contact with PHE 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227H SER 4.6 4.5 + - - +
229H PRO* 3.9 25.6 - - + -
307H THR* 4.0 28.0 - - + -
310H VAL* 2.6 51.9 + - + -
311H SER* 1.3 72.9 - - - +
313H PHE* 1.3 70.1 + - - +
329H LEU* 3.6 33.7 - - + -
330H LEU 3.1 11.9 - - - -
331H GLY* 4.0 6.7 - - - -
338H MET* 4.8 3.1 - - - -
340H VAL* 3.2 39.7 - - + -
384H GLU* 4.7 0.7 - - - +
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Residues in contact with PHE 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311H SER* 4.0 16.6 - - - -
312H PHE* 1.3 79.8 - - - +
314H LEU* 1.3 64.5 + - - +
315H VAL* 3.4 2.8 + - + +
328H ARG 3.7 0.5 - - - +
329H LEU* 3.8 5.1 - - - -
330H LEU* 3.1 41.4 + - + +
332H ILE* 4.7 8.7 - - + -
384H GLU* 2.6 36.3 - - + +
387H GLN* 4.1 16.6 - - + -
388H ILE* 3.4 50.3 - - + -
391H LEU* 4.1 27.1 - - + -
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Residues in contact with LEU 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H PHE* 1.3 70.6 - - - +
315H VAL* 1.3 67.6 + - - +
316H LYS* 5.7 4.5 - - + -
327H PRO* 5.2 3.6 - - + -
328H ARG 3.7 10.1 - - - +
329H LEU* 3.7 23.5 - - + +
342H GLU* 3.8 28.3 - - + +
381H GLN* 4.4 1.9 + - - +
382H THR* 3.9 14.7 + - - -
383H THR 5.4 0.2 + - - -
384H GLU* 4.4 4.1 + - - +
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Residues in contact with VAL 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H PHE 4.0 6.3 - - - +
314H LEU* 1.3 80.9 - - - +
316H LYS* 1.3 82.4 + - - +
317H GLU 4.7 1.1 - - - +
327H PRO* 3.5 1.0 - - - +
328H ARG* 2.8 57.5 + - + +
330H LEU* 3.9 27.8 - - + -
378H TYR* 4.8 2.5 - - - +
380H VAL* 3.3 34.8 - - + -
381H GLN 3.3 8.5 - - - +
382H THR* 4.0 8.1 - - + +
388H ILE* 4.8 2.5 - - + -
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Residues in contact with LYS 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314H LEU* 5.7 4.7 - - + -
315H VAL* 1.3 92.7 - - - +
317H GLU* 1.3 66.5 + - - +
318H LYS 3.4 2.1 + - - -
325H LEU* 3.5 41.4 + - + +
326H VAL 3.8 4.5 - - - -
327H PRO* 3.5 30.8 - - + +
380H VAL* 4.3 1.0 - - - -
381H GLN* 3.0 55.9 + - + +
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Residues in contact with GLU 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315H VAL* 4.2 1.4 - - + +
316H LYS* 1.3 72.3 - - - +
318H LYS* 1.3 66.3 + - - +
324H LYS 3.9 0.5 - - - +
325H LEU* 3.2 1.4 - - - -
326H VAL* 2.9 37.4 + - + +
328H ARG* 2.5 49.7 + - + +
339H ARG* 3.0 15.4 + - - -
378H TYR* 2.9 45.6 + - + +
379H SER 4.9 7.0 - - - +
380H VAL* 4.7 5.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il